I asked about this in MO's comments section (I actually knew that MO was incorrect, and was asking if one could turn off a single instance of the warning. It so happens that we cannot). In Tannin's response, however, he said this, "The PMOP check simply advises to place mods with conflicting scripts in the same order as the corresponding esp." This means that the warning is just that, a warning. It could be right, it could be dead wrong, it's just telling you to check.
MO provides detailed information on each mod is overwriting, and being overwritten by. You can, and should, check these individually. Then you can determine mod priority for yourself.
Nudedragon's post in MO's "Potential Mod Order Problem" was marked as the answer